single cell RNA profiling analysis of imaging-based spatial transcriptomics data
Project description
News (16/07/24)
- Update with comseg 1.4: Compatibility with SOPA : (https://gustaveroussy.github.io/sopa/tutorials/comseg/) + fix bug centroid
Support
If you have any questions relative to the package or bug, please open an issue in this repository.
ComSeg framework
A detail documentation is available at https://comseg.readthedocs.io/
Single cell spatial RNA profiling
ComSeg is an algorithm for single cell spatial RNA profiling in image-based transcriptomic data.
It takes as input a csv with the spot coordinates and output an anndata object with the genes expression and coordinates of each cell.
Citation
Defard, T., Laporte, H., Ayan, M. et al. A point cloud segmentation framework for image-based spatial transcriptomics. Commun Biol 7, 823 (2024). https://doi.org/10.1038/s42003-024-06480-3
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file comseg-1.8.2.tar.gz.
File metadata
- Download URL: comseg-1.8.2.tar.gz
- Upload date:
- Size: 33.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.0.0 CPython/3.8.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | b47debd0aa834e8526f4b09c269deee0ac740f8cc629ba5b211d13eb5c721803 |
|
| MD5 | aaa3307f3760d7e6d5d1fba46a659180 |
|
| BLAKE2b-256 | 89084e3c28e7c466b83739e7b007803966556042de99bdb220d21fdb6434380b |
File details
Details for the file ComSeg-1.8.2-py3-none-any.whl.
File metadata
- Download URL: ComSeg-1.8.2-py3-none-any.whl
- Upload date:
- Size: 37.2 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.0.0 CPython/3.8.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | d1885c9255d96c2bc84157ad8b94f13b2313261915ded7b50447be94df3ee66c |
|
| MD5 | fbaba7e7619111c58bdd2df2fca72148 |
|
| BLAKE2b-256 | 87555820f52cba66b9e5680e7c36391ca324ca46e56947ddaddb214658a06379 |
